STEM BIO-AI Explain Report
Target : yorkeccak/bio
Policy : default [ca-policy-1.0; mirror_only; authoritative_release]
Policy Mode: mirror-only in 1.7.5 — selected profile metadata is surfaced in artifacts, but authoritative scan scoring still follows deterministic runtime constants. Preview-only posture changes, including Stage 4 replication emphasis, do not change the formal score until a future read-through phase. Use `stem policy simulate` to preview governed score deltas and posture changes.
Score : 48 / 100 (T1 Quarantine)
Replic : 30 / 100 (R1)
========================================================================
S1_readme_bio_terms [DETECTED] (37 findings)
[001] README.md:2
finding_id: S1_readme_bio_terms:README.md:2:001
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "
"
reason : README exposes bio/medical vocabulary.
match : bio
[002] README.md:2
finding_id: S1_readme_bio_terms:README.md:2:002
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : ""
reason : README exposes bio/medical vocabulary.
match : bio
[003] README.md:3
finding_id: S1_readme_bio_terms:README.md:3:003
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "
"
reason : README exposes bio/medical vocabulary.
match : bio
[004] README.md:3
finding_id: S1_readme_bio_terms:README.md:3:004
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : ""
reason : README exposes bio/medical vocabulary.
match : bio
[005] README.md:4
finding_id: S1_readme_bio_terms:README.md:4:005
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "
"
reason : README exposes bio/medical vocabulary.
match : bio
[006] README.md:4
finding_id: S1_readme_bio_terms:README.md:4:006
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : ""
reason : README exposes bio/medical vocabulary.
match : bio
[007] README.md:5
finding_id: S1_readme_bio_terms:README.md:5:007
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "
"
reason : README exposes bio/medical vocabulary.
match : bio
[008] README.md:5
finding_id: S1_readme_bio_terms:README.md:5:008
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : ""
reason : README exposes bio/medical vocabulary.
match : bio
[009] README.md:8
finding_id: S1_readme_bio_terms:README.md:8:009
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "# Bio"
reason : README exposes bio/medical vocabulary.
match : Bio
[010] README.md:10
finding_id: S1_readme_bio_terms:README.md:10:010
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "Try the hosted version [here](https://bio.valyu.ai) 🙌"
reason : README exposes bio/medical vocabulary.
match : bio
[011] README.md:14
finding_id: S1_readme_bio_terms:README.md:14:011
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "> **Enterprise-grade biomedical research behind a chat interface** - Access PubMed, clinical trials, FDA drug labels, and run complex Python analyses through natural language. P..."
reason : README exposes bio/medical vocabulary.
match : clinical
[012] README.md:16
finding_id: S1_readme_bio_terms:README.md:16:012
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : ""
reason : README exposes bio/medical vocabulary.
match : Bio
[013] README.md:16
finding_id: S1_readme_bio_terms:README.md:16:013
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : ""
reason : README exposes bio/medical vocabulary.
match : bio
[014] README.md:18
finding_id: S1_readme_bio_terms:README.md:18:014
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "## Why Bio?"
reason : README exposes bio/medical vocabulary.
match : Bio
[015] README.md:20
finding_id: S1_readme_bio_terms:README.md:20:015
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "Traditional biomedical research and data is fragmented across dozens of databases and platforms. Bio changes everything by providing:"
reason : README exposes bio/medical vocabulary.
match : Bio
[016] README.md:22
finding_id: S1_readme_bio_terms:README.md:22:016
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "- **Comprehensive Medical Data** - PubMed articles, ClinicalTrials.gov data, FDA drug labels, and more"
reason : README exposes bio/medical vocabulary.
match : Medical
[017] README.md:25
finding_id: S1_readme_bio_terms:README.md:25:017
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "- **Interactive Visualizations** - Beautiful charts and dashboards for clinical data"
reason : README exposes bio/medical vocabulary.
match : clinical
[018] README.md:26
finding_id: S1_readme_bio_terms:README.md:26:018
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "- **Real-Time Intelligence** - Web search integration for breaking medical news"
reason : README exposes bio/medical vocabulary.
match : medical
[019] README.md:35
finding_id: S1_readme_bio_terms:README.md:35:019
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "- **Clinical Trials Database** - Search ClinicalTrials.gov for active and completed trials"
reason : README exposes bio/medical vocabulary.
match : Clinical
[020] README.md:38
finding_id: S1_readme_bio_terms:README.md:38:020
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "- **Interactive Charts** - Visualize clinical data, drug efficacy, patient outcomes"
reason : README exposes bio/medical vocabulary.
match : clinical
[021] README.md:38
finding_id: S1_readme_bio_terms:README.md:38:021
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "- **Interactive Charts** - Visualize clinical data, drug efficacy, patient outcomes"
reason : README exposes bio/medical vocabulary.
match : patient
[022] README.md:44
finding_id: S1_readme_bio_terms:README.md:44:022
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "- **Interactive Charts** - Create publication-ready visualizations of clinical data"
reason : README exposes bio/medical vocabulary.
match : clinical
[023] README.md:50
finding_id: S1_readme_bio_terms:README.md:50:023
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "Self-hosted mode is the recommended way to run Bio. It provides a complete local environment with:"
reason : README exposes bio/medical vocabulary.
match : Bio
[024] README.md:68
finding_id: S1_readme_bio_terms:README.md:68:024
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "git clone https://github.com/yorkeccak/bio.git"
reason : README exposes bio/medical vocabulary.
match : bio
[025] README.md:69
finding_id: S1_readme_bio_terms:README.md:69:025
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "cd bio"
reason : README exposes bio/medical vocabulary.
match : bio
[026] README.md:165
finding_id: S1_readme_bio_terms:README.md:165:026
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "- That's it! Bio will automatically detect and use it"
reason : README exposes bio/medical vocabulary.
match : Bio
[027] README.md:167
finding_id: S1_readme_bio_terms:README.md:167:027
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "3. **Use in Bio**"
reason : README exposes bio/medical vocabulary.
match : Bio
[028] README.md:216
finding_id: S1_readme_bio_terms:README.md:216:028
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "Try these powerful queries to see what Bio can do:"
reason : README exposes bio/medical vocabulary.
match : Bio
[029] README.md:218
finding_id: S1_readme_bio_terms:README.md:218:029
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "- "What are the latest clinical trials for CAR-T therapy in melanoma?""
reason : README exposes bio/medical vocabulary.
match : clinical
[030] README.md:222
finding_id: S1_readme_bio_terms:README.md:222:030
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "- "Analyze Phase 3 clinical trial data for immunotherapy drugs""
reason : README exposes bio/medical vocabulary.
match : clinical
[031] README.md:227
finding_id: S1_readme_bio_terms:README.md:227:031
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "- Keep all your medical research completely private"
reason : README exposes bio/medical vocabulary.
match : medical
[032] README.md:228
finding_id: S1_readme_bio_terms:README.md:228:032
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "- Perfect for sensitive patient data analysis"
reason : README exposes bio/medical vocabulary.
match : patient
[033] README.md:243
finding_id: S1_readme_bio_terms:README.md:243:033
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "The quickest way to get Bio running in production:"
reason : README exposes bio/medical vocabulary.
match : Bio
[034] README.md:260
finding_id: S1_readme_bio_terms:README.md:260:034
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "- No storage of sensitive medical data"
reason : README exposes bio/medical vocabulary.
match : medical
[035] README.md:279
finding_id: S1_readme_bio_terms:README.md:279:035
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "For bugs or feature requests, [open an issue](https://github.com/yorkeccak/bio/issues) or start a [discussion](https://github.com/yorkeccak/bio/discussions)."
reason : README exposes bio/medical vocabulary.
match : bio
[036] README.md:279
finding_id: S1_readme_bio_terms:README.md:279:036
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "For bugs or feature requests, [open an issue](https://github.com/yorkeccak/bio/issues) or start a [discussion](https://github.com/yorkeccak/bio/discussions)."
reason : README exposes bio/medical vocabulary.
match : bio
[037] README.md:296
finding_id: S1_readme_bio_terms:README.md:296:037
pattern : bio_terms_v1
evidence: confirmed_present
conf : high
snippet : "GitHub"
reason : README exposes bio/medical vocabulary.
match : bio
S1_clinical_boundary [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S1_clinical_boundary:.:0:001
pattern : clinical_boundary_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S1_clinical_boundary.
S1_H1_clinical_certainty_hype [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S1_H1_clinical_certainty_hype:.:0:001
pattern : hype_clinical_certainty_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S1_H1_clinical_certainty_hype.
S1_H2_regulatory_approval_hype [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S1_H2_regulatory_approval_hype:.:0:001
pattern : hype_regulatory_approval_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S1_H2_regulatory_approval_hype.
S1_H3_autonomous_replacement_hype [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S1_H3_autonomous_replacement_hype:.:0:001
pattern : hype_autonomous_replacement_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S1_H3_autonomous_replacement_hype.
S1_H4_breakthrough_marketing_hype [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S1_H4_breakthrough_marketing_hype:.:0:001
pattern : hype_breakthrough_marketing_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S1_H4_breakthrough_marketing_hype.
S1_H5_universal_generalization_hype [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S1_H5_universal_generalization_hype:.:0:001
pattern : hype_universal_generalization_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S1_H5_universal_generalization_hype.
S1_H6_perfect_accuracy_hype [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S1_H6_perfect_accuracy_hype:.:0:001
pattern : hype_perfect_accuracy_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S1_H6_perfect_accuracy_hype.
S1_R1_limitations_section [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S1_R1_limitations_section:.:0:001
pattern : limitations_section_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S1_R1_limitations_section.
S1_R2_regulatory_framework [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S1_R2_regulatory_framework:.:0:001
pattern : regulatory_framework_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S1_R2_regulatory_framework.
S1_R2_weak_regulatory_self_assertion [DETECTED] (1 finding)
[001] README.md:262
finding_id: S1_R2_weak_regulatory_self_assertion:README.md:262:001
pattern : weak_regulatory_self_assertion_v1
evidence: confirmed_present
conf : high
snippet : "- HIPAA-compliant architecture (when self-hosted)"
reason : Self-asserted privacy/compliance language detected without stronger regulatory-framework evidence.
match : HIPAA-compliant
S1_R2_unsupported_legal_or_compliance_claim [DETECTED] (1 finding)
[001] README.md:262
finding_id: S1_R2_unsupported_legal_or_compliance_claim:README.md:262:001
pattern : unsupported_legal_or_compliance_claim_v1
evidence: confirmed_present
conf : high
snippet : "- HIPAA-compliant architecture (when self-hosted)"
reason : Legal, privacy, or compliance claim detected without supporting governance or security-grounding evidence in reviewed sources.
claim : HIPAA-compliant
grounding_present : False
S1_R4_demographic_bias_boundary [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S1_R4_demographic_bias_boundary:.:0:001
pattern : demographic_bias_boundary_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S1_R4_demographic_bias_boundary.
S1_R5_reproducibility_provisions [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S1_R5_reproducibility_provisions:.:0:001
pattern : reproducibility_provisions_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S1_R5_reproducibility_provisions.
S3_T1_workflow_files [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S3_T1_workflow_files:.:0:001
pattern : workflow_presence_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S3_T1_workflow_files.
S3_T2_domain_tests [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S3_T2_domain_tests:.:0:001
pattern : domain_tests_bio_terms_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S3_T2_domain_tests.
S3_T3_changelog_release_hygiene [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S3_T3_changelog_release_hygiene:.:0:001
pattern : changelog_presence_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S3_T3_changelog_release_hygiene.
S3_T3_changelog_bugfix_evidence [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S3_T3_changelog_bugfix_evidence:.:0:001
pattern : changelog_bugfix_terms_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S3_T3_changelog_bugfix_evidence.
S3_B1_dependency_manifest [DETECTED] (3 findings)
[001] package-lock.json
finding_id: S3_B1_dependency_manifest:package-lock.json:0:001
pattern : dependency_manifest_presence_v1
evidence: confirmed_present
conf : high
snippet : "package-lock.json"
reason : Dependency or environment manifest exists.
[001] package.json
finding_id: S3_B1_dependency_manifest:package.json:0:001
pattern : dependency_manifest_presence_v1
evidence: confirmed_present
conf : high
snippet : "package.json"
reason : Dependency or environment manifest exists.
[001] pnpm-lock.yaml
finding_id: S3_B1_dependency_manifest:pnpm-lock.yaml:0:001
pattern : dependency_manifest_presence_v1
evidence: confirmed_present
conf : high
snippet : "pnpm-lock.yaml"
reason : Dependency or environment manifest exists.
S3_B1_data_source_language [DETECTED] (2 findings)
[001] README.md:22
finding_id: S3_B1_data_source_language:README.md:22:001
pattern : data_source_terms_v1
evidence: confirmed_present
conf : high
snippet : "- **Comprehensive Medical Data** - PubMed articles, ClinicalTrials.gov data, FDA drug labels, and more"
reason : Data source, dataset citation, IRB, or provenance language detected.
match : ClinicalTrials
[002] README.md:35
finding_id: S3_B1_data_source_language:README.md:35:002
pattern : data_source_terms_v1
evidence: confirmed_present
conf : high
snippet : "- **Clinical Trials Database** - Search ClinicalTrials.gov for active and completed trials"
reason : Data source, dataset citation, IRB, or provenance language detected.
match : ClinicalTrials
S3_B2_bias_limitations [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S3_B2_bias_limitations:.:0:001
pattern : bias_limitations_v2
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S3_B2_bias_limitations.
S3_B2_measurement_evidence [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S3_B2_measurement_evidence:.:0:001
pattern : bias_measurement_terms_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S3_B2_measurement_evidence.
S3_B3_coi_funding [DETECTED] (1 finding)
[001] README.md:281
finding_id: S3_B3_coi_funding:README.md:281:001
pattern : coi_funding_v1
evidence: confirmed_present
conf : high
snippet : "## Acknowledgments"
reason : COI, funding, sponsor, or acknowledgement language detected.
match : Acknowledgments
S2_package_bio_terms [DETECTED] (2 findings)
[001] package.json:2
finding_id: S2_package_bio_terms:package.json:2:001
pattern : package_bio_terms_v1
evidence: confirmed_present
conf : high
snippet : ""name": "bio","
reason : Package metadata exposes bio/medical vocabulary.
match : bio
[002] package.json:5
finding_id: S2_package_bio_terms:package.json:5:002
pattern : package_bio_terms_v1
evidence: confirmed_present
conf : high
snippet : ""description": "Enterprise-grade biomedical research AI chatbot with access to PubMed, clinical trials, FDA drug labels, and Python code execution","
reason : Package metadata exposes bio/medical vocabulary.
match : clinical
R2R_D5_single_external_service_dependency [DETECTED] (8 findings)
[001] .env.example:24
finding_id: R2R_D5_single_external_service_dependency:.env.example:24:001
pattern : single_external_service_dependency_v1
evidence: confirmed_present
conf : medium
snippet : "VALYU_API_KEY=valyu_your_api_key_here"
reason : Required external service API key detected for a named workflow dependency.
provider : Valyu
env_var : VALYU_API_KEY
required_signal : True
[002] .env.example:38
finding_id: R2R_D5_single_external_service_dependency:.env.example:38:002
pattern : single_external_service_dependency_v1
evidence: confirmed_present
conf : medium
snippet : "DAYTONA_API_KEY=your_daytona_api_key_here"
reason : Required external service API key detected for a named workflow dependency.
provider : Daytona
env_var : DAYTONA_API_KEY
required_signal : True
[001] README.md:23
finding_id: R2R_D5_single_external_service_dependency:README.md:23:001
pattern : single_external_service_dependency_v1
evidence: confirmed_present
conf : high
snippet : "- **One Unified Search** - Powered by Valyu's specialized biomedical data API"
reason : Named external service provider is presented as part of the core repository workflow.
provider : Valyu
line_role : provider_dependency_claim
[002] README.md:60
finding_id: R2R_D5_single_external_service_dependency:README.md:60:002
pattern : single_external_service_dependency_v1
evidence: confirmed_present
conf : high
snippet : "- Valyu API key (get one at [platform.valyu.ai](https://platform.valyu.ai))"
reason : Named external service provider is presented as part of the core repository workflow.
provider : Valyu
line_role : provider_dependency_claim
[003] README.md:61
finding_id: R2R_D5_single_external_service_dependency:README.md:61:003
pattern : single_external_service_dependency_v1
evidence: confirmed_present
conf : high
snippet : "- [Daytona](https://www.daytona.io) API key - used for secure sandboxed Python code execution (get one at [app.daytona.io](https://app.daytona.io))"
reason : Named external service provider is presented as part of the core repository workflow.
provider : Daytona
line_role : provider_dependency_claim
[004] README.md:48
finding_id: R2R_D5_single_external_service_dependency:README.md:48:004
pattern : single_external_service_dependency_v1
evidence: confirmed_present
conf : high
snippet : "## Quick Start (Self-Hosted)"
reason : Local or self-host claims coexist with required external service dependencies.
providers : ['Daytona', 'Valyu']
line_role : local_or_self_host_claim
provider_count : 2
[005] README.md:50
finding_id: R2R_D5_single_external_service_dependency:README.md:50:005
pattern : single_external_service_dependency_v1
evidence: confirmed_present
conf : high
snippet : "Self-hosted mode is the recommended way to run Bio. It provides a complete local environment with:"
reason : Local or self-host claims coexist with required external service dependencies.
providers : ['Daytona', 'Valyu']
line_role : local_or_self_host_claim
provider_count : 2
[006] README.md:51
finding_id: R2R_D5_single_external_service_dependency:README.md:51:006
pattern : single_external_service_dependency_v1
evidence: confirmed_present
conf : high
snippet : "- **No authentication required** - Auto-login as dev user"
reason : Local or self-host claims coexist with required external service dependencies.
providers : ['Daytona', 'Valyu']
line_role : local_or_self_host_claim
provider_count : 2
C1_hardcoded_credentials [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: C1_hardcoded_credentials:.:0:001
pattern : credential_pattern_v2
evidence: not_found_in_reviewed_sources
conf : medium
reason : No hardcoded credential evidence detected for C1_hardcoded_credentials.
C2_dependency_pinning [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: C2_dependency_pinning:.:0:001
pattern : loose_dependency_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No loose dependency evidence detected.
C3_dead_or_deprecated_patient_adjacent_paths [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: C3_dead_or_deprecated_patient_adjacent_paths:.:0:001
pattern : deprecated_patient_metadata_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for C3_dead_or_deprecated_patient_adjacent_paths.
C4_exception_handling_clinical_adjacent_paths [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: C4_exception_handling_clinical_adjacent_paths:.:0:001
pattern : fail_open_exception_v2
evidence: not_found_in_reviewed_sources
conf : medium
reason : No fail-open exception handler detected in executable Python code.
BIO_smiles_surface_integrity [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: BIO_smiles_surface_integrity:.:0:001
pattern : bio_smiles_surface_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No malformed or suspicious SMILES-like strings detected by conservative surface checks.
BIO_smiles_rdkit_validation [NOT_APPLICABLE] (1 finding)
[001] (repository)
finding_id: BIO_smiles_rdkit_validation:.:0:001
pattern : bio_smiles_rdkit_invalid_v1
evidence: not_applicable
conf : high
reason : RDKit optional validation lane unavailable in current environment.
lane : A1_optional_rdkit
BIO_smiles_parser_guard [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: BIO_smiles_parser_guard:.:0:001
pattern : bio_smiles_parser_guard_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No missing None/invalid guards detected after SMILES parser calls.
BIO_silent_mock_fallback [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: BIO_silent_mock_fallback:.:0:001
pattern : bio_silent_mock_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No silent mock or simulated-data fallback patterns detected in production code paths.
BIO_trace_manifest [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: BIO_trace_manifest:.:0:001
pattern : bio_trace_manifest_file_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No traceability manifest or runtime audit-log schema surface detected.
BIO_run_trace [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: BIO_run_trace:.:0:001
pattern : bio_run_trace_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No risky subprocess or os.system bio-tool execution patterns detected.
S4_container_environment [DETECTED] (1 finding)
[001] Dockerfile
finding_id: S4_container_environment:Dockerfile:0:001
pattern : container_file_v1
evidence: confirmed_present
conf : high
snippet : "Dockerfile"
reason : Container or compose file exists.
S4_make_reproduce_target [ABSENT] (1 finding)
[001] (repository)
finding_id: S4_make_reproduce_target:.:0:001
pattern : make_reproduce_target_v1
evidence: confirmed_missing
conf : medium
reason : No Makefile detected.
S4_environment_lock_evidence [DETECTED] (2 findings)
[001] package-lock.json
finding_id: S4_environment_lock_evidence:package-lock.json:0:001
pattern : environment_lock_file_v1
evidence: confirmed_present
conf : high
snippet : "package-lock.json"
reason : Environment, dependency, or lock manifest detected.
[001] pnpm-lock.yaml
finding_id: S4_environment_lock_evidence:pnpm-lock.yaml:0:001
pattern : environment_lock_file_v1
evidence: confirmed_present
conf : high
snippet : "pnpm-lock.yaml"
reason : Environment, dependency, or lock manifest detected.
S4_exact_dependency_pins_or_hashes [DETECTED] (2 findings)
[001] package-lock.json
finding_id: S4_exact_dependency_pins_or_hashes:package-lock.json:0:001
pattern : exact_pin_or_hash_v1
evidence: confirmed_present
conf : high
snippet : "package-lock.json"
reason : Lock manifest with exact dependency resolution detected.
[001] pnpm-lock.yaml
finding_id: S4_exact_dependency_pins_or_hashes:pnpm-lock.yaml:0:001
pattern : exact_pin_or_hash_v1
evidence: confirmed_present
conf : high
snippet : "pnpm-lock.yaml"
reason : Lock manifest with exact dependency resolution detected.
S4_readme_reproducibility_section [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S4_readme_reproducibility_section:.:0:001
pattern : readme_repro_heading_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : README exists but no reproducibility or replication section heading was detected.
S4_checksum_files [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S4_checksum_files:.:0:001
pattern : checksum_file_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S4_checksum_files.
S4_dataset_url [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S4_dataset_url:.:0:001
pattern : dataset_url_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : Documentation exists but no dataset URL or data source URL was detected.
S4_model_weight_url_or_checksum [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S4_model_weight_url_or_checksum:.:0:001
pattern : model_weight_url_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : Documentation exists but no model artifact URL/checksum evidence was detected.
S4_citation_cff [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S4_citation_cff:.:0:001
pattern : citation_cff_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S4_citation_cff.
S4_license_restriction [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S4_license_restriction:.:0:001
pattern : license_restriction_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : License/readme/docs surfaces exist but no restriction language was detected.
S4_cli_entrypoint [ABSENT] (1 finding)
[001] (repository)
finding_id: S4_cli_entrypoint:.:0:001
pattern : cli_entrypoint_v1
evidence: confirmed_missing
conf : medium
reason : No package metadata or Python AST surface detected.
S4_seed_setting [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S4_seed_setting:.:0:001
pattern : ast_seed_setting_stage4_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No deterministic seed setting evidence detected by AST summary.
S4_runnable_examples [NOT_DETECTED] (1 finding)
[001] (repository)
finding_id: S4_runnable_examples:.:0:001
pattern : runnable_example_file_v1
evidence: not_found_in_reviewed_sources
conf : medium
reason : No evidence detected for S4_runnable_examples.
========================================================================
Bio Deterministic Diagnostics
SMILES Surface Integrity not_detected=1
SMILES RDKit Validation not_applicable=1
SMILES Parser Guard not_detected=1
Silent Mock Fallback not_detected=1
Traceability Manifest Surface not_detected=1
Bio Subprocess Run Trace not_detected=1
========================================================================
Regulatory Traceability Assistant
Regulatory basis note
Aligned to current official source classes as of May 2026: EU AI Act (Regulation (EU) 2024/1689), FDA QMSR, FDA AI-enabled device guidance themes, and IMDRF SaMD/GMLP frameworks.
This is a traceability aid, not a compliance or clearance determination.
stage_1
EU_AI_ACT_ARTICLE_13: signal_only (mapping=weak, evidence=weak)
note: Boundary, intended-use, and limitation language is relevant to transparency scaffolding only.
COMPLIANCE_CLAIM_GROUNDING_SIGNAL: signal_only (mapping=weak_moderate, evidence=weak)
note: Legal or compliance claims without supporting governance evidence are relevant to transparency and quality-system review, not compliance proof.
stage_2r
IMDRF_CLINICAL_CONTEXT_BOUNDARY_SIGNAL: signal_only (mapping=weak_moderate, evidence=moderate)
note: Repository-local contradiction and boundary signals are relevant to clinical-context traceability, not clinical validation.
stage_3
EU_AI_ACT_ARTICLE_10: signal_only (mapping=weak, evidence=weak)
note: Provenance and bias signals are relevant to data-governance review, but do not verify execution quality.
stage_4
EU_AI_ACT_ARTICLE_12: partially_aligned (mapping=moderate, evidence=moderate)
note: Reproducibility and trace manifests support record-keeping scaffolding, not operational logging completeness.
summary Structural signals partially align with traceability scaffolding. This remains a pre-audit traceability aid, not a compliance determination.
========================================================================
AIRI Coverage
covered_count 8
detector_scope_total 32
coverage_rate 0.25
bundle_scope curated_medical_clinical_subset
upstream_snapshot 2026-04-23
covered examples:
- 24.01.03 | Safe exploration problem with widely deployed AI assistants | covered_by=C4_exception_handling_clinical_adjacent_paths
- 24.04.01 | Physical and Psychological Harms | covered_by=C2_dependency_pinning
- 33.01.05 | Privacy and security | covered_by=C2_dependency_pinning
known gaps in bundle:
- 65.03.03 | Reidentification
- 70.02.02 | Misinformation — hallucination of clinical knowledge
========================================================================
Audit Freshness
review_after_days 45
expires_on 2026-06-29
freshness_basis clinical_adjacent_short_cycle
change_triggered_reaudit_now False
change_triggered_reasons none
trigger_examples git_commit_changed, readme_or_docs_claim_surface_changed, dependency_manifest_changed, dataset_or_model_reference_changed
========================================================================
AST Signal Summary
files_total 0
files_considered 0
files_parsed 0
files_skipped_size 0
syntax_errors 0
file_limit_exceeded False
test_functions 0
assertion_tests 0
public_functions 0
docstring_functions 0
annotated_functions 0
seed_settings 0
argparse_cli False
portable_model_loading 0
fail_open_handlers 0
========================================================================
Stage 4 Replication Rubric
S4_container_environment 10 / 10 Container or compose file exists.
S4_make_reproduce_target 0 / 10 No Makefile detected.
S4_environment_lock_evidence 10 / 10 Environment, dependency, or lock manifest detected.
S4_exact_dependency_pins_or_hashes 10 / 10 Exact dependency pin or hash evidence detected.
S4_readme_reproducibility_section 0 / 10 README exists but no reproducibility or replication section heading was detected.
S4_checksum_files 0 / 10 No evidence detected for S4_checksum_files.
S4_dataset_url 0 / 10 Documentation exists but no dataset URL or data source URL was detected.
S4_model_weight_url_or_checksum 0 / 10 Documentation exists but no model artifact URL/checksum evidence was detected.
S4_citation_cff 0 / 5 No evidence detected for S4_citation_cff.
S4_license_restriction 0 / 0 No license/use restriction language detected.
S4_cli_entrypoint 0 / 5 No package metadata or Python AST surface detected.
S4_seed_setting 0 / 5 No deterministic seed setting detected.
S4_runnable_examples 0 / 5 No evidence detected for S4_runnable_examples.
stage_4_raw_total 30 / 100 Raw Stage 4 rubric total. Stage 4 is reported separately and does not alter final score.
========================================================================
Reasoning Diagnostics
version stem-bio-ai-reasoning-v1.3.2
mode diagnostic_only
final_score_override False
weights uncalibrated_initial_priors_pending_benchmark_calibration
evidence_budget supported
confidence_envelope unknown
lane_coherence heuristic_mixed
uncertainty_budget review_advised
evidence_risk_gate within_heuristic_gate
========================================================================
DISCLAIMER: Evidence-surface pre-screen only.
Not clinical certification, regulatory clearance, or medical advice.